FossilDatabaseProject
Meagan Crowson, Kristin Grandstaff, Sarah Powell, Andrea Redmond, Brecken Roquemore
4/26/2021
Creation of fossil dataframe
library("data.table")
data.table(Fossil_Database)## Fossil_Type Name Genus Species Country
## 1: Ammonites
## 2: MOLAM0001 Graspedites N/A Russia
## 3: MOLAM0002 N/A N/A Nepal
## 4: MOLAM0003 Polished Belemnite N/A Russia
## 5: MOLAM0004 Eleganticeras elegantulum England
## 6: MOLAM0005 Metalegoceras tschernyschewi Indonesia
## 7: MOLAM0006 N/A N/A United Kingdom
## 8: MOLAM0007 Hypocladiscites subaratus plantus Indonesia
## 9: MOLAM0008 N/A N/A USA
## 10: MOLAM0009 Lanceolites compactus Indonesia
## 11: MOLAM0010 54 N/A Morocco
## 12: MOLAM0011 Tissotia obesa Peru
## 13: MOLAM0012 Microdoceras N/A United Kingdom
## 14: MOLAM0013 Laevaptychus latus England
## 15: MOLAM0014 N/A N/A United Kingdom
## 16: MOLAM0015 N/A N/A USA
## 17: MOLAM0016 Muensteroceras parallelum USA
## 18: MOLAM0017 N/A N/A United Kingdom
## 19: MOLAM0018 N/A N/A Morocco
## 20: Mazon_Creek
## 21: MAZCRK0001 N/A N/A USA
## 22: MAZCRK0002 N/A N/A USA
## 23: MAZCRK0003 N/A N/A USA
## 24: MAZCRK0004 N/A N/A USA
## 25: MAZCRK0005 N/A N/A USA
## 26: MAZCRK0006 N/A N/A USA
## 27: MAZCRK0007 N/A N/A USA
## 28: MAZCRK0008 N/A N/A USA
## 29: MAZCRK0009 N/A N/A USA
## 30: MAZCRK0010 N/A N/A USA
## 31: MAZCRK0011 N/A N/A USA
## 32: MAZCRK0012 N/A N/A USA
## 33: MAZCRK0013 N/A N/A USA
## 34: MAZCRK0014 N/A N/A USA
## 35: MAZCRK0015 N/A N/A USA
## 36: MAZCRK0016 N/A N/A USA
## 37: MAZCRK0017 N/A N/A USA
## 38: MAZCRK0018 N/A N/A USA
## 39: MAZCRK0019 N/A N/A USA
## 40: MAZCRK0020 N/A N/A USA
## 41: MAZCRK0021 N/A N/A USA
## 42: MAZCRK0022 N/A N/A USA
## 43: MAZCRK0023 N/A N/A USA
## 44: MAZCRK0024 N/A N/A USA
## 45: MAZCRK0025 N/A N/A USA
## 46: MAZCRK0026 N/A N/A USA
## 47: MAZCRK0027 N/A N/A USA
## 48: MAZCRK0028 N/A N/A USA
## 49: MAZCRK0029 N/A N/A USA
## 50: MAZCRK0030 N/A N/A USA
## 51: MAZCRK0031 N/A N/A USA
## 52: MAZCRK0032 N/A N/A USA
## 53: MAZCRK0033 N/A N/A USA
## 54: MAZCRK0034 N/A N/A USA
## 55: MAZCRK0035 N/A N/A USA
## 56: MAZCRK0036 N/A N/A USA
## 57: MAZCRK0037 N/A N/A USA
## Fossil_Type Name Genus Species Country
## State_or_Region
## 1:
## 2: N/A
## 3: Annapurna, Mustang
## 4: Tarstan Region
## 5: North Yorkshire, Whitby Cannonball
## 6: Timor, Noe Bihati
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## 21: Illinois
## 22: Illinois
## 23: Illinois
## 24: Illinois
## 25: Illinois
## 26: Illinois
## 27: Illinois
## 28: Illinois
## 29: Illinois
## 30: Illinois
## 31: Illinois
## 32: Illinois
## 33: Illinois
## 34: Illinois
## 35: Illinois
## 36: Illinois
## 37: Illinois
## 38: Illinois
## 39: Illinois
## 40: Illinois
## 41: Illinois
## 42: Illinois
## 43: Illinois
## 44: Illinois
## 45: Illinois
## 46: Illinois
## 47: Illinois
## 48: Illinois
## 49: Illinois
## 50: Illinois
## 51: Illinois
## 52: Illinois
## 53: Illinois
## 54: Illinois
## 55: Illinois
## 56: Illinois
## 57: Illinois
## State_or_Region
## State_or_Region.1
## 1:
## 2: N/A
## 3: Annapurna, Mustang
## 4: Tarstan Region
## 5: North Yorkshire, Whitby Cannonball
## 6: Timor, Noe Bihati
## 7: Charmouth
## 8: Timor, Noe Bihati
## 9: Wyoming
## 10: Timor, Noe Bihati
## 11: N/A
## 12: Cajamarca
## 13: Black Ven, Lyme Regis
## 14: Westbury, Wiltshire
## 15: North Yorkshire, Nr. Whitby Kettleness
## 16: Little Glasses Creek, Marshall County, Little Glasses Creek, Oklahoma
## 17: Jackson County, Indiana
## 18: Charmouth
## 19: N/A
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## 21: Illinois
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## State_or_Region.1
## Formation
## 1:
## 2: N/A
## 3: N/A
## 4: N/A
## 5: N/A
## 6: N/A
## 7: N/A
## 8: N/A
## 9: N/A
## 10: N/A
## 11: N/A
## 12: N/A
## 13: N/A
## 14: N/A
## 15: N/A
## 16: N/A
## 17: Rockford Limestone
## 18: N/A
## 19: N/A
## 20:
## 21: Mazon Creek
## 22: Mazon Creek
## 23: Mazon Creek
## 24: Mazon Creek
## 25: Mazon Creek
## 26: Mazon Creek
## 27: Mazon Creek
## 28: Mazon Creek
## 29: Mazon Creek
## 30: Mazon Creek
## 31: Mazon Creek
## 32: Mazon Creek
## 33: Mazon Creek
## 34: Mazon Creek
## 35: Mazon Creek
## 36: Mazon Creek
## 37: Mazon Creek
## 38: Mazon Creek
## 39: Mazon Creek
## 40: Mazon Creek
## 41: Mazon Creek
## 42: Mazon Creek
## 43: Mazon Creek
## 44: Mazon Creek
## 45: Mazon Creek
## 46: Mazon Creek
## 47: Mazon Creek
## 48: Mazon Creek
## 49: Mazon Creek
## 50: Mazon Creek
## 51: Mazon Creek
## 52: Mazon Creek
## 53: Mazon Creek
## 54: Mazon Creek
## 55: Mazon Creek
## 56: Mazon Creek
## 57: Mazon Creek
## Formation
## Time_Period Dates
## 1:
## 2: Jurassic N/A
## 3: Jurassic ~185 MYA
## 4: Late Jurassic 165 MYA
## 5: Lower Jurassic 180 MYA
## 6: Lower Permian N/A
## 7: N/A N/A
## 8: Norian, Triassic 227-208.5 MYA
## 9: N/A N/A
## 10: Lower Triassic Smithian N/A
## 11: N/A N/A
## 12: Upper Cretaceous Coniacian N/A
## 13: N/A N/A
## 14: Kimmeridgian Jurassic 157 MYA
## 15: Bifrons Zone, Commune Subzone, Upper Lias, Lower Jurassic 180 MYA
## 16: N/A N/A
## 17: N/A 325 MYA
## 18: N/A N/A
## 19: N/A N/A
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## Time_Period Dates
## Value Collector Common_Name Descriptor
## 1:
## 2: N/A R. Unzha Kostroma N/A N/A
## 3: N/A N/A Shaligram N/A
## 4: N/A Dr. Utt polished Belemite N/A
## 5: N/A N/A N/A N/A
## 6: N/A N/A N/A N/A
## 7: N/A N/A N/A N/A
## 8: N/A N/A N/A Mojsisovics
## 9: N/A N/A Belemite Guard N/A
## 10: N/A N/A N/A N/A
## 11: N/A N/A Goniatite N/A
## 12: N/A N/A N/A N/A
## 13: N/A N/A N/A N/A
## 14: N/A N. Zachariades N/A Parkinson
## 15: N/A N/A Whitby Snakestone N/A
## 16: N/A Dr. Utt N/A N/A
## 17: N/A N/A N/A N/A
## 18: N/A N/A N/A N/A
## 19: N/A N/A Goniatite N/A
## 20: N/A
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## Value Collector Common_Name Descriptor
## Miscellaneous
## 1:
## 2: N/A
## 3: Kali_Gandaki_River
## 4: N/A
## 5: polished upper lias, falciferum subzone
## 6: N/A
## 7: Belemite
## 8: N/A
## 9: N/A
## 10: N/A
## 11: N/A
## 12: N/A
## 13: N/A
## 14: aptychii: paired calcereous plates forming part of the jaw apparatus in certain ammonite families
## 15: N/A
## 16: Rhynocholites
## 17: Mississippian Pd
## 18: Pyritized
## 19: N/A
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## Miscellaneous
## Images
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## Imagesdata## function (..., list = character(), package = NULL, lib.loc = NULL,
## verbose = getOption("verbose"), envir = .GlobalEnv, overwrite = TRUE)
## {
## fileExt <- function(x) {
## db <- grepl("\\.[^.]+\\.(gz|bz2|xz)$", x)
## ans <- sub(".*\\.", "", x)
## ans[db] <- sub(".*\\.([^.]+\\.)(gz|bz2|xz)$", "\\1\\2",
## x[db])
## ans
## }
## names <- c(as.character(substitute(list(...))[-1L]), list)
## if (!is.null(package)) {
## if (!is.character(package))
## stop("'package' must be a character string or NULL")
## if (any(package %in% "base"))
## warning("datasets have been moved from package 'base' to package 'datasets'")
## if (any(package %in% "stats"))
## warning("datasets have been moved from package 'stats' to package 'datasets'")
## package[package %in% c("base", "stats")] <- "datasets"
## }
## paths <- find.package(package, lib.loc, verbose = verbose)
## if (is.null(lib.loc))
## paths <- c(path.package(package, TRUE), if (!length(package)) getwd(),
## paths)
## paths <- unique(normalizePath(paths[file.exists(paths)]))
## paths <- paths[dir.exists(file.path(paths, "data"))]
## dataExts <- tools:::.make_file_exts("data")
## if (length(names) == 0L) {
## db <- matrix(character(), nrow = 0L, ncol = 4L)
## for (path in paths) {
## entries <- NULL
## packageName <- if (file_test("-f", file.path(path,
## "DESCRIPTION")))
## basename(path)
## else "."
## if (file_test("-f", INDEX <- file.path(path, "Meta",
## "data.rds"))) {
## entries <- readRDS(INDEX)
## }
## else {
## dataDir <- file.path(path, "data")
## entries <- tools::list_files_with_type(dataDir,
## "data")
## if (length(entries)) {
## entries <- unique(tools::file_path_sans_ext(basename(entries)))
## entries <- cbind(entries, "")
## }
## }
## if (NROW(entries)) {
## if (is.matrix(entries) && ncol(entries) == 2L)
## db <- rbind(db, cbind(packageName, dirname(path),
## entries))
## else warning(gettextf("data index for package %s is invalid and will be ignored",
## sQuote(packageName)), domain = NA, call. = FALSE)
## }
## }
## colnames(db) <- c("Package", "LibPath", "Item", "Title")
## footer <- if (missing(package))
## paste0("Use ", sQuote(paste("data(package =", ".packages(all.available = TRUE))")),
## "\n", "to list the data sets in all *available* packages.")
## else NULL
## y <- list(title = "Data sets", header = NULL, results = db,
## footer = footer)
## class(y) <- "packageIQR"
## return(y)
## }
## paths <- file.path(paths, "data")
## for (name in names) {
## found <- FALSE
## for (p in paths) {
## tmp_env <- if (overwrite)
## envir
## else new.env()
## if (file_test("-f", file.path(p, "Rdata.rds"))) {
## rds <- readRDS(file.path(p, "Rdata.rds"))
## if (name %in% names(rds)) {
## found <- TRUE
## if (verbose)
## message(sprintf("name=%s:\t found in Rdata.rds",
## name), domain = NA)
## thispkg <- sub(".*/([^/]*)/data$", "\\1", p)
## thispkg <- sub("_.*$", "", thispkg)
## thispkg <- paste0("package:", thispkg)
## objs <- rds[[name]]
## lazyLoad(file.path(p, "Rdata"), envir = tmp_env,
## filter = function(x) x %in% objs)
## break
## }
## else if (verbose)
## message(sprintf("name=%s:\t NOT found in names() of Rdata.rds, i.e.,\n\t%s\n",
## name, paste(names(rds), collapse = ",")),
## domain = NA)
## }
## if (file_test("-f", file.path(p, "Rdata.zip"))) {
## warning("zipped data found for package ", sQuote(basename(dirname(p))),
## ".\nThat is defunct, so please re-install the package.",
## domain = NA)
## if (file_test("-f", fp <- file.path(p, "filelist")))
## files <- file.path(p, scan(fp, what = "", quiet = TRUE))
## else {
## warning(gettextf("file 'filelist' is missing for directory %s",
## sQuote(p)), domain = NA)
## next
## }
## }
## else {
## files <- list.files(p, full.names = TRUE)
## }
## files <- files[grep(name, files, fixed = TRUE)]
## if (length(files) > 1L) {
## o <- match(fileExt(files), dataExts, nomatch = 100L)
## paths0 <- dirname(files)
## paths0 <- factor(paths0, levels = unique(paths0))
## files <- files[order(paths0, o)]
## }
## if (length(files)) {
## for (file in files) {
## if (verbose)
## message("name=", name, ":\t file= ...", .Platform$file.sep,
## basename(file), "::\t", appendLF = FALSE,
## domain = NA)
## ext <- fileExt(file)
## if (basename(file) != paste0(name, ".", ext))
## found <- FALSE
## else {
## found <- TRUE
## zfile <- file
## zipname <- file.path(dirname(file), "Rdata.zip")
## if (file.exists(zipname)) {
## Rdatadir <- tempfile("Rdata")
## dir.create(Rdatadir, showWarnings = FALSE)
## topic <- basename(file)
## rc <- .External(C_unzip, zipname, topic,
## Rdatadir, FALSE, TRUE, FALSE, FALSE)
## if (rc == 0L)
## zfile <- file.path(Rdatadir, topic)
## }
## if (zfile != file)
## on.exit(unlink(zfile))
## switch(ext, R = , r = {
## library("utils")
## sys.source(zfile, chdir = TRUE, envir = tmp_env)
## }, RData = , rdata = , rda = load(zfile,
## envir = tmp_env), TXT = , txt = , tab = ,
## tab.gz = , tab.bz2 = , tab.xz = , txt.gz = ,
## txt.bz2 = , txt.xz = assign(name, read.table(zfile,
## header = TRUE, as.is = FALSE), envir = tmp_env),
## CSV = , csv = , csv.gz = , csv.bz2 = ,
## csv.xz = assign(name, read.table(zfile,
## header = TRUE, sep = ";", as.is = FALSE),
## envir = tmp_env), found <- FALSE)
## }
## if (found)
## break
## }
## if (verbose)
## message(if (!found)
## "*NOT* ", "found", domain = NA)
## }
## if (found)
## break
## }
## if (!found) {
## warning(gettextf("data set %s not found", sQuote(name)),
## domain = NA)
## }
## else if (!overwrite) {
## for (o in ls(envir = tmp_env, all.names = TRUE)) {
## if (exists(o, envir = envir, inherits = FALSE))
## warning(gettextf("an object named %s already exists and will not be overwritten",
## sQuote(o)))
## else assign(o, get(o, envir = tmp_env, inherits = FALSE),
## envir = envir)
## }
## rm(tmp_env)
## }
## }
## invisible(names)
## }
## <bytecode: 0x7f8fd08c3ae0>
## <environment: namespace:utils>a <- 